miRNA: 3'- caUGCGU-------GCGGUUCGU-------------ACuGUUGCGG- -5'
miRNA: 3'- -CAUGCgUG-----CGGUU-CGUACUGU--UGCGG- -5'
miRNA: 3'- -CAuGCGUGCGG-------------UUCGu---------ACUGUUGCGg -5'
miRNA: 3'- -CAUGCgUGCGGUUCGUACUGuug--CGg -5'
Results 21 - 24 of 24 are showing below:
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| ID | Location | Perfect MFE.* | RefSeq Acc. | strand |
Start Position
|
R_P_ratio# | P value |
| Predicted miRNA align pattern | |||||||
| 14672 | 5' | -52.3 | NC_003525.1 | + | 8122 | 0.68 | 0.798291 |
|
Target: 5'- -gACGCAcuggugcCGCUGAGCGcauccggugaaacUGuCAGCGCCg -3' miRNA: 3'- caUGCGU-------GCGGUUCGU-------------ACuGUUGCGG- -5' |
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| 14672 | 5' | -52.3 | NC_003525.1 | + | 7317 | 0.68 | 0.79037 |
|
Target: 5'- aGUACGgGCuugucGCCAGuGUAUGACGauAUGCCc -3' miRNA: 3'- -CAUGCgUG-----CGGUU-CGUACUGU--UGCGG- -5' |
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| 14672 | 5' | -52.3 | NC_003525.1 | + | 6356 | 0.66 | 0.879007 |
|
Target: 5'- aGU-CGCACGCUguucccacgucuuGAGCcggugcauguUGACAGCGCg -3' miRNA: 3'- -CAuGCGUGCGG-------------UUCGu---------ACUGUUGCGg -5' |
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| 14672 | 5' | -52.3 | NC_003525.1 | + | 2612 | 0.66 | 0.863756 |
|
Target: 5'- gGUGCG-ACGUCAGGCGUGGCuaucaGUa -3' miRNA: 3'- -CAUGCgUGCGGUUCGUACUGuug--CGg -5' |
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Note:
When operating RNAhybrid, the pipeline first calculates the perfect minimum free energy (Perfect mfe *) of a putative miRNA when the entire putative miRNA binds to a perfectly complementary target site, then it calculates the minimum free energy of RNA duplex (mfe of the miRNA/mRNA duplex), abbreviated as Rd_mfe. An alignment for which the Rd_mfe to its correspondent Perfect mfe ratio (R_P_ratio #) is more than 66% is regarded as a positive alignment as described by Krek et al. (21). The P_value is calculated by RNAhybrid.
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